source: nappy/trunk/nappy/nappy_api.py @ 3991

Subversion URL: http://proj.badc.rl.ac.uk/svn/ndg/nappy/trunk/nappy/nappy_api.py@3991
Revision 3991, 17.3 KB checked in by astephen, 12 years ago (diff)

Converted all global_atts to lists of key,value pairs so order can be maintained.

Line 
1"""
2nappy_api.py
3============
4
5Top-level API module that allows user to access most of the useful stuff in
6nappy. API examples:
7
8 1. Working with NASA Ames file objects
9 2. Converting between formats (NASA Ames, NetCDF and CSV)
10 3. Comparing NASA Ames files (and/or CSV files)
11 4. General NASA Ames utilities
12
13 1. Working with NASA Ames file objects
14
15# Start python interactive shell
16$ python
17
18# Import the nappy package
19import nappy
20
21# Let's open a NASA Ames file and examine its contents
22f = nappy.openNAFile("data_files/2010.na")
23
24# Get number of header lines
25n_lines = f.getNumHeaderLines()
26
27# Get Organisation from header
28org = f.getOrg()
29# Get the Normal Comments (SCOM) lines.
30norm_comms = f.getNormalComments()
31
32# Get the Special Comments (SCOM) lines.
33spec_comms = f.getSpecialComments()
34
35# Get a list of metadata for all main (non-auxiliary or independent) variables
36var_list = getVariables()
37
38# Get Auxiliary variable metadata for auxiliary variable number 2
39(variable, units, miss, scale) = f.getAuxVariable(2)
40
41# Get scale factor for primary variable number 3
42scale_factor = f.getScaleFactor(3)
43
44# Get missing value for primary variable number 1
45missing = f.getMissingValue(1)
46
47# Let's get the contents dictionary of the whole file
48na_dict = f.getNADict()
49
50# Let's write the na_dict object to a new NASA Ames file
51fout = openNAFile("test_outputs/mytest.na", mode="w", na_dict=na_dict)
52fout.write()
53fout.close()
54
55 2. Converting between formats (NASA Ames, NetCDF and CSV)
56
57# Let's convert a NASA Ames file into a NetCDF file, and add some of our own global attributes
58glob_atts = [("Project", "Really important scientific project involving worms"),
59             ("Errata": "I meant worm holes!")]
60na_file = "data_files/1020.na"
61nc_file = "test_outputs/try_1020.nc"
62nappy.convertNAToNC(na_file, nc_file, global_attributes=glob_atts)
63
64# Let's convert a NASA Ames file to a CSV and add an annotation column to explain the header
65nappy.convertNAToCSV(na_file, annotation=True)
66
67# Let's read a NetCDF and write one (or more) output NASA Ames files,
68# but only including and variables "temp" and "ozone". Also let's write
69# the output using tabs as the delimiters and a float format of "%6.3f".
70nappy.convertNCToNA("data_files/test1.nc", "test_outputs/test1nc.na",
71              var_ids=("temp", "ozone"), delimiter="\t", float_format="%6.3f")
72 
73# Let's convert a NetCDF file to one (or more) CSV files and don't write the header at all
74nappy.convertNCToCSV("data_files/test1.nc", "test_outputs/test1nc_no_header.csv",
75                     no_header=True)
76
77# Let's take some in-memory CDMS objects and write them to one, or more, NASA Ames file(s).
78# We need to give it a list of cdms variables and a global attributes list of tuples/lists.
79# We also want to instruct nappy to overwrite the content of its
80# MNAME (Mission Name) header line with our specific mission name.
81# Also, tell nappy to write the output to NASA Ames file format index (FFI) 2310
82# because we know it is compatible.
83nappy.convertCDMSObjectsToNA([cdms_var_1, cdms_var_2], [("Institute", "British Atmospheric Data Centre")],
84              na_file="test_outputs/cdms_to_na.na",
85              na_items_to_override={"MNAME": "Atlantic Divergence Mission 2009"},
86              requested_ffi=2310)
87
88# Let's take a list of cdms variables and a global attributes list and write
89# them to a CSV file.
90nappy.convertCDMSObjectsToCSV(cdms_vars, global_atttributes, csv_file)
91
92# Let's take a NASA Ames dictionary object, and write it to a NetCDF file
93nappy.writeNADictToNC(na_dict, nc_file, mode="w")
94
95# Let's try and write a second na_dict object to the same NetCDF file using mode="a".
96nappy.writeNADictToNC(na_dict_2, nc_file, mode="a")
97
98# Now let's read in a NASA Ames file and convert the contents in-memory into
99# CDMS objects so that we can manipulate them with NetCDF-compatible tools
100(cdms_vars_primary, cdms_vars_aux, global_attributes) = nappy.readCDMSObjectsFromNA(na_file)
101
102# Actually, I only want to get a single variable from that file, so I'll try
103temp_var = getCDMSVariableFromNA(na_file, "temperature")
104
105 3. Comparing NASA Ames files (and/or CSV files)
106
107# I'd like to compare a NASA Ames and CSV file to check they are the same.
108# It will allow for different formatting of numbers as long as the values
109# are the same. Compare both header and body by setting as True (default).
110result = nappy.compareNA(na_file, csv_file, header=True, body=True,
111            number_clever=True, delimiter_1="    ", delimiter_2=",")
112
113 4. General NASA Ames utilities
114
115# Get the FFI from a NASA Ames file
116ffi = nappy.readFFI(na_file)
117
118# Given a NASA Ames dictionary (na_dict) get an appropriate FFI.
119ffi = nappy.chooseFFI(na_dict)
120
121
122"""
123
124# Import standard library modules
125
126# Import third-party software
127try:
128    import cdms2 as cdms
129except:
130    try:
131        import cdms
132    except:
133        print "WARNING: You cannot use NAPpy's NetCDF conversion tools as your system does not have CDMS installed, or it is not in your sys.path."
134        cdms = False
135
136# Import local modules
137import nappy.utils.common_utils
138import nappy.utils.compare_na
139
140# Bring some utils into the API
141compareNA = nappy.utils.compare_na.compareNA
142readFFI = nappy.utils.common_utils.readFFI
143chooseFFI = nappy.utils.common_utils.chooseFFI
144getNAFileClass = nappy.utils.common_utils.getNAFileClass
145__version__ = nappy.utils.common_utils.getVersion()
146default_delimiter = nappy.utils.common_utils.getDefault("default_delimiter")
147default_float_format = nappy.utils.common_utils.getDefault("default_float_format")
148
149
150def openNAFile(filename, mode="r", na_dict=None):
151    """
152    Function wrapper around the NASA Ames File classes. Any NASA Ames
153    file can be opened through this function and the appropriate read or
154    write NASA Ames File class instance is returned.
155    """
156    if mode == "r":
157        ffi = readFFI(filename)
158        return apply(getNAFileClass(ffi), (filename, mode))
159
160    elif mode == "w":
161        if na_dict.has_key('FFI') and type(na_dict['FFI']) == type(3):
162            ffi = na_dict['FFI']
163        else:
164            ffi = chooseFFI(na_dict)
165            na_dict['FFI'] = ffi
166            print "\nFormat identified as:", ffi   
167        return apply(getNAFileClass(ffi), (filename,), {"mode":mode, "na_dict":na_dict})
168    else:
169        raise Exception("File mode not recognised '" + mode + "'.")
170
171
172def convertNAToNC(na_file, nc_file=None, mode="w", variables=None, aux_variables=None,
173                 global_attributes=[("Conventions", "CF-1.0")],
174                 time_units=None, time_warning=True,
175                 rename_variables={}):
176    """
177    Takes a NASA Ames file and converts to a NetCDF file. Options are:
178
179    na_file - the input NASA Ames file.
180    nc_file - name for the output NetCDF file (default is to replace ".na" from NASA Ames
181              file with ".nc").
182    mode - is the file mode, either "w" for write or "a" for append
183    variables - is a list of variable names that you wish to be converted. If not set then
184              nappy will attempt to convert all files.
185    aux_var_list - is a list of auxiliary variables names that you wish to be converted.
186              If not set then nappy will use any compatible variables it finds as
187              auxiliary variables.
188    global_attributes - is a list of global attributes to add to the output file.
189    rename_variables - is a dictionary of {old_name: new_name} variable ID pairs that nappy
190              should use to rename variables before it writes them to file. 
191    time_units - is a valid time units string such as "hours since 2003-04-30 10:00:00" to
192              use for time units if there is a valid time axis.
193    time_warning - suppresses the time units warning for invalid time units if set to False.
194    """
195    arg_dict = vars()
196    for arg_out in ("nc_file", "mode"):
197        del arg_dict[arg_out]
198
199    convertor = apply(nappy.nc_convertor.na_to_nc.NAToNC, [], arg_dict)
200    convertor.convert()
201    if nc_file == None:
202        nc_file = nappy.utils.getFileNameWithNewExtension(na_file, "nc")
203    convertor.writeNCFile(nc_file, mode)
204    return nc_file   
205 
206
207def convertNAToCSV(na_file, csv_file=None, annotation=False, no_header=False):
208    """
209    Reads in a NASA Ames file and writes it out a new CSV file which is identical to the
210    input file except that commas are used as the delimiter. Arguments are:
211
212    na_file - NASA Ames file path
213    csv_file - CSV file path (default is to replace ".na" from NASA Ames file with ".csv").
214    annotation - if set to True write the output file with an additional left-hand column
215                 describing the contents of each header line.
216    no_header - if set to True then only the data blocks are written to file.
217    """
218    fin = openNAFile(na_file)
219    fin.readData()
220    na_dict = fin.getNADict()
221    fin.close()
222
223    if csv_file == None:
224        csv_file = nappy.utils.getFileNameWithNewExtension(nc_file, "csv")
225    fout = openNAFile(csv_file, "w", na_dict=na_dict)
226    fout.write(delimiter=",", annotation=annotation)
227    fout.close()
228    return True
229
230
231def convertNCToNA(nc_file, na_file=None, var_ids=None, na_items_to_override={},
232            only_return_file_names=False, exclude_vars=[],
233            requested_ffi=None, delimiter=default_delimiter, float_format=default_float_format, 
234            size_limit=None, annotation=False, no_header=False):
235    """
236    Takes a NetCDF file and converts the contents to one or more NASA Ames files.
237    Arguments are:
238
239    nc_file - is the name of input file (NetCDF).
240    na_file - is the name of output file (default is to replace ".nc" from NASA Ames
241              file with ".na"). If multiple files produced then this name will be used
242              as the base name.
243    var_ids - is a list of variables (as ids) to include in the output file(s).
244    na_items_to_override - is a dictionary of {key: value} pairs to overwrite in output
245              files. Typically the keys are in: 
246              ("DATE", "RDATE", "ANAME", "MNAME","ONAME", "ORG", "SNAME", "VNAME".)
247    only_return_file_names - if set to True then only return a list of file names that
248              would be written (i.e. don't convert actual file).
249    exclude_vars - is a list of variables (as ids) to exclude in the output file(s).
250    requested_ffi - is the NASA Ames File Format Index (FFI) you wish to write to. Note
251              that there are only limited options available depending on the data
252              structures found.
253    delimiter - the delimiter you wish to use between data items in the output file such
254              as "   ", "\t" or ",".
255    float_format - a python formatting string such as "%s", "%g" or "%5.2f" used for
256              formatting floats when written to file.
257    size_limit - if format FFI is 1001 then chop files up into size_limit rows of data.
258    annotation - if set to True write the output file with an additional left-hand column
259              describing the contents of each header line.
260    no_header - if set to True then only the data blocks are written to file.
261    """
262    arg_dict = vars()
263    for arg_out in ("na_file", "only_return_file_names", "delimiter", "float_format", 
264                    "size_limit", "annotation", "no_header"):
265        del arg_dict[arg_out]
266
267    if na_file == None:
268        na_file =  nappy.utils.getFileNameWithNewExtension(nc_file, "na")
269
270    convertor = apply(nappy.nc_convertor.nc_to_na.NCToNA, [], arg_dict)
271    convertor.convert()
272
273    # If user only wants files then only give them that
274    if only_return_file_names == True:
275        return convertor.constructNAFileNames(na_file)
276    else:
277        convertor.writeNAFiles(na_file, delimiter=delimiter, float_format=float_format, 
278                               size_limit=size_limit, annotation=annotation, no_header=no_header)
279        print convertor.output_message
280        output_files_written = convertor.output_files_written
281        print output_files_written
282        return output_files_written
283
284   
285def convertNCToCSV(nc_file, csv_file=None, **arg_dict):
286    """
287    Reads in a NetCDF file and writes the data out to a CSV file following the
288    NASA Ames standard.
289    """
290    if csv_file == None:
291        csv_file = nappy.utils.getFileNameWithNewExtension(nc_file, "csv")
292        arg_dict["na_file"] = csv_file
293        arg_dict["delimiter"] = ","
294 
295    return apply(convertNCToNA, [nc_file], arg_dict)
296   
297
298def convertCDMSObjectsToNA(cdms_vars, global_attributes, na_file, 
299              na_items_to_override={}, requested_ffi=None, delimiter=default_delimiter, 
300              float_format=default_float_format, size_limit=None, annotation=False, no_header=False):
301    """
302    Takes a list of cdms variables and a list of global attributes and
303    writes them to one or more NASA Ames files. Arguments are:
304 
305    cdms_vars - is a list of CDMS variables
306    global_attributes - is a list of (key, value) pairs for header
307    na_items_to_override - is a dictionary of {key: value} pairs to overwrite in
308                output files. Typically the keys are in: 
309                ("DATE", "RDATE", "ANAME", "MNAME","ONAME", "ORG", "SNAME", "VNAME", "SCOM", "NCOM".)
310    requested_ffi - is the NASA Ames File Format Index (FFI) you wish to write to.
311                Note that there are only limited options available depending on the data
312                structures found.
313    delimiter - the delimiter you wish to use between data items in the output file
314                such as "   ", "\t" or ",".
315    float_format - a python formatting string such as "%s", "%g" or "%5.2f" used for
316                formatting floats when written to file.
317    size_limit - if format FFI is 1001 then chop files up into size_limit rows of data.
318    annotation - if set to True write the output file with an additional left-hand
319                column describing the contents of each header line.
320    no_header - if set to True then only the data blocks are written to file.
321    """
322    import nappy.nc_interface.cdms_objs_to_na_file
323    convertor = nappy.nc_interface.cdms_objs_to_na_file.CDMSObjectsToNAFile(cdms_vars, global_attributes=global_attributes, 
324                        na_items_to_override=na_items_to_override, requested_ffi=requested_ffi)
325    convertor.convert()
326    na_files = convertor.writeNAFiles(na_file, delimiter=delimiter, float_format=float_format, 
327                                      annotation=annotation, no_header=no_header) 
328    return convertor.output_files_written
329
330
331def convertCDMSObjectsToCSV(cdms_vars, global_attributes, csv_file, **arg_dict):
332    """
333    Takes a list of cdms variables and a global attributes list and
334    writes them to one or more CSV files.
335    """
336    arg_dict["delimiter"] = ","
337    return apply(convertCDMSObjectsToNA, [cdms_vars, global_attributes, csv_file], arg_dict)
338
339
340def writeNADictToNC(na_dict, nc_file, mode="w"):
341    """
342    Writes an NASA Ames dictionary object called na_dict to a NetCDF file called nc_file.
343    Can set mode="a" or mode="w" to either append to existing nc_file or write new one.
344    Note that mode="a" might not always work.
345    """
346    # Note, this needs to pretend that the na_dict exists, do this by instantiating NACore and cheating...
347    import nappy.na_file.na_core
348    na_file_obj = nappy.na_file.na_core.NACore()
349    na_file_obj.setNADict(na_dict)
350    # Fake up some required methods
351    def fakeCaller():pass
352    na_file_obj.readData = fakeCaller
353    import nappy.nc_interface.na_to_cdms
354    convertor = nappy.nc_interface.na_to_cdms.NAToCDMS(na_file_obj)
355    (cdms_primary_vars, cdms_aux_vars, global_attributes) = convertor.convert()
356
357    # Now write them out
358    fout = cdms.open(nc_file, mode=mode)
359    for var in (cdms_primary_vars + cdms_aux_vars):
360        fout.write(var)
361
362    # Write global attributes
363    for (att, value) in global_attributes:
364        setattr(fout, att, value)
365       
366    fout.close()
367    print "NetCDF file '%s' written successfully." % file_name
368    return True
369
370
371def readCDMSObjectsFromNA(na_file):
372    """
373    Reads the NASA Ames file and converts to CDMS objects.
374    Returns a tuple containing:
375      * a list of primary NASA Ames variables as CDMS variables
376      * a list of auxiliary NASA Ames variables as CDMS variables,
377      * a list of global attributes
378    """
379    cdms_var_list = []
380    global_attributes = {}
381
382    # Open the NA file
383    na_file_obj = openNAFile(na_file)
384    import nappy.nc_interface.na_to_cdms
385    convertor = nappy.nc_interface.na_to_cdms.NADictToCdmsObjects(na_file_obj)
386    (cdms_vars_primary, cdms_vars_aux, global_attributes) = convertor.convert()
387    return (cdms_vars_primary, cdms_vars_aux, global_attributes)
388
389
390def getCDMSVariableFromNA(na_file, var):
391    """
392    Returns a CDMS variable object (TransientVariable) identified by the var argument which
393    can either be an integer index in the list of variables or the name of the variable.
394    The variable is created from the variables found in the NASA Ames file na_file.
395    """
396    na_file_obj = openNAFile(na_file)
397    import nappy.nc_interface.na_to_cdms
398    convertor = nappy.nc_interface.na_to_cdms.NADictToCdmsObjects(na_file_obj, variables=[var])
399    (cdms_primary_vars, cdms_aux_vars, global_attributes) = convertor.convert()
400    # Must now be a primary var
401    return cdms_primary_vars[0]
402
403
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